= bio-sradl

SRA is an archive of NGS data provided by NIH. Is possible to download the data from a browser or using a traditional ftp program. This package is a convenient way to download or explore the archive without knowing anything about ftp connection. Is possible to download single read archive or a bunch of them or download all the reads from an Experiment, a Study, a Sample or a Run.

== HowToUse

an example of SRA directory: /sra/sra-instant/reads/ByRun/litesra/SRR/SRR027/SRR027883

biosradl list list the content of the root archive (/sra/sra-instant/reads)

biosradl list ByExp|ByStudy|ByRun|BySample list the sub directories of these macro groups (/sra/sra-instant/reads/ByRun)

biosradl list ByRun:027 list the content of (/sra/sra-instant/reads/BuRun/litesra/SRR/SRR027), that means list all the runs of

Download works in a similar way. The user can provide the single name of a run

biosradl download SRR027883 it will create a file named SRR027883.lite.sra in the current directory

or activate a parallel download of all the SRAs in the specified tree: biosradl download ByRun:027

is possible to download different sets in one shot: biosradl ByRun:027,ByExp:001

By default the archives are searched in the lite form. To look for regular archive, it's a bit tricky: biosradl list SRR:066998 --lite=false or biosradl list SRR:066998 -l false

Note: for developers take a look to the declaration of the above option, you can refer to it from your method using the hash "options"

== Contributing to bio-sradl

• Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
• Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
• Fork the project
• Start a feature/bugfix branch
• Commit and push until you are happy with your contribution
• Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
• Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

== Copyright

Copyright (c) 2011 Raoul J.P. Bonnal. See LICENSE.txt for further details.